OneAngstrom – Page 110

Take Full Control of Molecular Presentations by Stopping at Key Frames

When you’re preparing a molecular animation to explain your research, showcase a protein-ligand interaction, or present a simulation workflow, timing is everything. A smooth animation is great—but what if you want to pause and provide more context, discuss a mechanism,…

Why Saving Molecular Structures Isn’t Just ‘Save As’

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When working on molecular simulations, structural predictions, or drug design pipelines, you often find yourself needing to export your molecular models for use in other tools. Whether it’s to share your structure with colleagues, analyze it with a different software,…

Spotting the Right Render Preset in SAMSON Using NSL

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When working with complex molecular models, keeping track of how elements are displayed can become challenging. Whether highlighting active sites, customizing visual styles for presentations, or debugging display issues, efficiently selecting and manipulating render presets is key to productivity when…

Struggling to Export Your Molecular Models? Here’s What You Can Do

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If you’re a molecular modeler working with multiple tools and file formats, you’ve probably bumped into this common issue: exporting your models in the right format for a collaborator, a publication, or a specific simulation package. Whether you need .pdb…

Solvation Tips for Coarse-Grained Systems: Avoiding Pitfalls with Martini Water

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One of the trickiest steps when setting up a coarse-grained (CG) system for molecular dynamics (MD) simulations is solvation — especially when using popular CG force fields like Martini. A common frustration among researchers is finding out, only after running…

Making Your Molecular Projects Portable: Embedding Files and Folders in SAMSON

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One constant challenge in molecular modeling is project portability. Whether you’re collaborating with colleagues, moving projects across machines, or preparing simulations for publication, keeping everything together can be frustrating. Files often get separated, paths break, or dependencies go missing. Fortunately,…

Visualizing Molecular Motion in Reverse Can Clarify Hidden Transitions

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When analyzing molecular simulations or transitions between conformations, understanding the complete trajectory—including its reverse—can offer essential insights. While most users typically examine forward motions, playing animations in reverse can reveal details such as intermediate conformations, relaxation events, or path symmetries…

How to Create Custom Index Groups in GROMACS Simulations with SAMSON

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If you’ve ever run GROMACS simulations, you probably know that defining the right index groups can be crucial. Whether you’re setting up pulling groups for umbrella sampling, customizing restraints, or extracting specific analysis from your trajectory, index groups give you…

Working with label visibility in SAMSON using NSL

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When working on complex molecular models in SAMSON, it’s easy for your screen to become cluttered—especially when multiple labels are displayed. Whether you’re tracking molecular IDs, distances, or other annotations, label visibility can quickly become overwhelming. What if there was…

Avoiding Misleading Results in Protein Pathways: Why Energy Setup Matters

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When exploring conformational transitions in proteins, it’s tempting to dive straight into sampling and path search. But many molecular modelers have encountered a frustrating issue: unrealistic or noisy paths that seem physically implausible. A common cause? Skipping proper energy setup…